Update packages.yaml format and support configuration updates

The YAML config for paths and modules of external packages has
changed: the new format allows a single spec to load multiple
modules. Spack will automatically convert from the old format
when reading the configs (the updates do not add new essential
properties, so this change in Spack is backwards-compatible).

With this update, Spack cannot modify existing configs/environments
without updating them (e.g. “spack config add” will fail if the
configuration is in a format that predates this PR). The user is
prompted to do this explicitly and commands are provided. All
config scopes can be updated at once. Each environment must be
updated one at a time.

lib/spack/llnl/util/filesystem.py

@@ -2,7 +2,6 @@
 # Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
-
 import collections
 import errno
 import hashlib
@@ -377,17 +376,17 @@ def install(src, dest):
     copy(src, dest, _permissions=True)
 
 
-def resolve_link_target_relative_to_the_link(l):
+def resolve_link_target_relative_to_the_link(link):
     """
     os.path.isdir uses os.path.exists, which for links will check
     the existence of the link target. If the link target is relative to
     the link, we need to construct a pathname that is valid from
     our cwd (which may not be the same as the link's directory)
     """
-    target = os.readlink(l)
+    target = os.readlink(link)
     if os.path.isabs(target):
         return target
-    link_dir = os.path.dirname(os.path.abspath(l))
+    link_dir = os.path.dirname(os.path.abspath(link))
     return os.path.join(link_dir, target)
 
 
@@ -1570,6 +1569,19 @@ def can_access_dir(path):
     return os.path.isdir(path) and os.access(path, os.R_OK | os.X_OK)
 
 
+@memoized
+def can_write_to_dir(path):
+    """Return True if the argument is a directory in which we can write.
+
+    Args:
+        path: path to be tested
+
+    Returns:
+        True if ``path`` is an writeable directory, else False
+    """
+    return os.path.isdir(path) and os.access(path, os.R_OK | os.X_OK | os.W_OK)
+
+
 @memoized
 def files_in(*search_paths):
     """Returns all the files in paths passed as arguments.
@@ -1683,3 +1695,18 @@ def prefixes(path):
         pass
 
     return paths
+
+
+def md5sum(file):
+    """Compute the MD5 sum of a file.
+
+    Args:
+        file (str): file to be checksummed
+
+    Returns:
+        MD5 sum of the file's content
+    """
+    md5 = hashlib.md5()
+    with open(file, "rb") as f:
+        md5.update(f.read())
+    return md5.digest()